Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices

05 June 2019, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space, as well as the physical meaning of the reduced dimensional axes, are discussed.


Dimensionality reduction
Reaction Coordinates
Molecular Dynamics


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